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Conditional Reasoning with Subjective Logic 
Jøsang, Audun (Journal article / Tidsskriftartikkel / SubmittedVersion, 2009)
Conditional inference plays a central role in logical and Bayesian reasoning, and is used in a wide range of applications. It basically consists of expressing conditional relationship between parent and child propositions, ...
Leakage Tolerant, Noise Immune domino logic for circuit design in the ultra deep sub-micron CMOS technology for haigh fan-in gates 
Peiravi, Ali; Moradi, Farshad; Wisland, Dag T (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells 
M Blomberg, K E; Boucheron, Nicole; Lindvall, Jessica M; Yu, Liang; Raberger, Julia; Berglöf, Anna; Ellmeier, Wilfried; Smith, CI E (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-like T-cell development. We have characterized the transcriptome ...
A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis 
Skotheim, Rolf I; Thomassen, Gard O; Eken, Marthe; Lind, Guro E; Micci, Francesca; Ribeiro, Franclim R; Cerveira, Nuno; Teixeira, Manuel R; Heim, Sverre; Rognes, Torbjørn; Lothe, Ragnhild A (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal ...
Large-scale inference of the point mutational spectrum in human segmental duplications 
Nakken, Sigve; Rødland, Einar A; Rognes, Torbjørn; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background Recent segmental duplications are relatively large (≥ 1 kb) genomic regions of high sequence identity (≥ 90%). They cover approximately 4–5% of the human genome and play important roles in gene ...
The mathematics of tanning 
Thingnes, Josef; Øyehaug, Leiv; Hovig, Eivind; Omholt, Stig W (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background The pigment melanin is produced by specialized cells, called melanocytes. In healthy skin, melanocytes are sparsely spread among the other cell types in the basal layer of the epidermis. Sun ...
The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts 
Nakken, Sigve; Rognes, Torbjørn; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as G-quadruplexes or G4 DNA. The enrichment of these motifs in key chromosomal regions has suggested ...
Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays 
Thomassen, Gard O Sundby; Rowe, Alexander D.; Lagesen, Karin; Lindvall, Jessica Margareta; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, ...
Genome dynamics in major bacterial pathogens 
Ambur, Ole Herman; Davidsen, Tonje; Frye, Stephan Alfons; Balasingham, Seetha; Lagesen, Karin; Rognes, Torbjørn; Tønjum, Tone (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Pathogenic bacteria continuously encounter multiple forms of stress in their hostile environments, which leads to DNA damage. With the new insight into biology offered by genome sequences, the elucidation of the gene content ...
Online Reputation Systems for the Health Sector 
Jøsang, Audun (Journal article / Tidsskriftartikkel / SubmittedVersion, 2008)
People who are seeking medical advice and care often find it difficult to obtain reliable information about the quality and competence of health service providers. While transparent quality evaluation of products and ...
Compo: composite motif discovery using discrete models 
Sandve, Geir K; Abul, Osman; Drabløs, Finn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2008)
Background Computational discovery of motifs in biomolecular sequences is an established field, with applications both in the discovery of functional sites in proteins and regulatory sites in DNA. In recent ...
GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data 
Lyng, Heidi; Lando, Malin; Brøvig, Runar S; Svendsrud, Debbie H; Johansen, Morten; Galteland, Eivind; Brustugun, Odd T; Meza-Zepeda, Leonardo A; Myklebost, Ola; Kristensen, Gunnar B; Hovig, Eivind; Stokke, Trond (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2008)
Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers ...
Validation of oligoarrays for quantitative exploration of the transcriptome 
Nygaard, Vigdis; Liu, Fang; Holden, Marit; Kuo, Winston P; Trimarchi, Jeff; Ohno-Machado, Lucila; Cepko, Connie L; Frigessi, Arnoldo; Glad, Ingrid K; van de Wiel, A M; Hovig, Eivind; Lyng, Heidi (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2008)
Background Oligoarrays have become an accessible technique for exploring the transcriptome, but it is presently unclear how absolute transcript data from this technique compare to the data achieved with ...
iRefIndex: A consolidated protein interaction database with provenance 
Razick, Sabry; Magklaras, George; Donaldson, Ian M (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2008)
Background Interaction data for a given protein may be spread across multiple databases. We set out to create a unifying index that would facilitate searching for these data and that would group together ...
Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors 
Baumbusch, LO; Aarøe, J; Johansen, FE; Hicks, J; Sun, H; Bruhn, L; Gunderson, K; Naume, B; Kristensen, VN; Liestøl, K; Børresen-Dale, A-L; Lingjærde, OC (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2008)
Background Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the ...
Salutogenic community building 
Viravong, Khamphira (Journal article / Tidsskriftartikkel, 2007)
A 'new' approach to community building is based on the concept of salutogenesis (a proactive approach to health promotion and prevention). Increasing organisational focus on sustaining healthy work forces requires a coherent ...
Designing quality management systems with minimal management commitment 
Øgland, Petter (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
In literature on quality management design it is common knowledge that quality management will not work without management commitment. But, not always is it possible to achieve management commitment, so what to do then? ...
Microarray-based method for detection of unknown genetic modifications 
Tengs, Torstein; Kristoffersen, Anja B; Berdal, Knut G; Thorstensen, Tage; Butenko, Melinka A; Nesvold, Håvard; Holst-Jensen, Arne (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
Background Due to the increased use of genetic modifications in crop improvement, there is a need to develop effective methods for the detection of both known and unknown transgene constructs in plants. We ...
Bovine milk in human nutrition – a review 
Haug, Anna; Høstmark, Arne T; Harstad, Odd M (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
Milk and milk products are nutritious food items containing numerous essential nutrients, but in the western societies the consumption of milk has decreased partly due to claimed negative health effects. The content of ...
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates 
Liu, Fang; Jenssen, Tor-Kristian; Trimarchi, Jeff; Punzo, Claudio; Cepko, Connie L; Ohno-Machado, Lucila; Hovig, Eivind; Patrick Kuo, Winston (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
Background High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based ...
Metabolic mapping by use of high-resolution magic angle spinning1H MR spectroscopy for assessment of apoptosis in cervical carcinomas 
Lyng, Heidi; Sitter, Beathe; Bathen, Tone F; Jensen, Line R; Sundfør, Kolbein; Kristensen, Gunnar B; Gribbestad, Ingrid S (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
Background High-resolution magic angle proton magnetic resonance spectroscopy (HR1H MAS MRS) provides a broad metabolic mapping of intact tumor samples and allows for microscopy investigations of the samples ...
Mapping of oxidative stress responses of human tumor cells following photodynamic therapy using hexaminolevulinate 
Cekaite, Lina; Peng, Qian; Reiner, Andrew; Shahzidi, Susan; Tveito, Siri; Furre, Ingegerd E; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
Background Photodynamic therapy (PDT) involves systemic or topical administration of a lesion-localizing photosensitizer or its precursor, followed by irradiation of visible light to cause singlet ...
Low-Complexity Distributed Multibase Transmission and Scheduling 
Skjevling, Hilde; Gesbert, David; Hjørungnes, Are (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
This paper addresses the problem of base station coordination and cooperation in wireless networks with multiple base stations. We present a distributed approach to downlink multibase beamforming, which allows for the ...
RNAmmer: consistent and rapid annotation of ribosomal RNA genes 
Lagesen, K; Hallin, P; Rødland, Einar Andreas; Staerfeldt, HH; Rognes, T; Ussery, DW (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes ...
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats 
Dalhus, Bjørn; Helle, Ina Høydal; Backe, Paul Hoff; Alseth, Ingrun; Rognes, Torbjørn; Bjørås, Magnar; Lærdahl, Jon Kristen (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
3-methyladenine DNA glycosylases initiate repair of cytotoxic and promutagenic alkylated bases in DNA. We demonstrate by comparative modelling that Bacillus cereus AlkD belongs to a new, fifth, structural superfamily of ...
LP based heuristics for the multiple knapsack problem with assignment restrictions 
Dahl, Geir; Foldnes, Njål (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2006)
Starting with a problem in wireless telecommunication, we are led to study the multiple knapsack problem with assignment restrictions. This problem is NP-hard. We consider special cases and their computational complexity. ...
Assessment of routine surveillance data as a tool to investigate measles outbreaks in Mozambique 
Jani, Jagrati V; Jani, Ilesh V; Araújo, Carolina; Sahay, Sundeep; Barreto, Jorge; Bjune, Gunnar (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2006)
Background Measles remains a major public health problem in Mozambique despite significant efforts to control the disease. Currently, health authorities base their outbreak control on data from the routine ...
Gene expressions and copy numbers associated with metastatic phenotypes of uterine cervical cancer 
Lyng, Heidi; Brøvig, Runar S; Svendsrud, Debbie H; Holm, Ruth; Kaalhus, Olav; Knutstad, Kjetil; Oksefjell, Halldis; Sundfør, Kolbein; Kristensen, Gunnar B; Stokke, Trond (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2006)
Background A better understanding of the development of metastatic disease and the identification of molecular markers for cancer spread would be useful for the design of improved treatment strategies. ...
Multilocus analysis of SNP and metabolic data within a given pathway 
Kristensen, Vessela N; Tsalenko, Anya; Geisler, Jurgen; Faldaas, Anne; Grenaker, Grethe I; Lingjærde, Ole C; Fjeldstad, Ståle; Yakhini, Zohar; Lønning, Per E; Børresen-Dale, Anne-Lise (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2006)
Background Complex traits, which are under the influence of multiple and possibly interacting genes, have become a subject of new statistical methodological research. One of the greatest challenges facing ...
Computational prediction of microRNAs encoded in viral and other genomes 
Thomassen, Gard O. S.; Rosok, Oystein; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2006)
We present an overview of selected computational methods for microRNA prediction. It is especially aimed at viral miRNA detection. As the number of microRNAs increases and the range of genomes encoding miRNAs expands, it ...
A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD 
Alseth, Ingrun; Rognes, Torbjørn; Lindbäck, Toril; Solberg, Inger; Robertsen, Kristin; Kristiansen, Knut Ivan; Mainieri, Davide; Lillehagen, Lucy; Kolstø, Anne-Brit; Bjørås, Magnar (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2006)
Soil bacteria are heavily exposed to environmental methylating agents such as methylchloride and may have special requirements for repair of alkylation damage on DNA. We have used functional complementation of an Escherichia ...
Assessing immunization data quality from routine reports in Mozambique 
Mavimbe, João C; Braa, Jørn; Bjune, Gunnar (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2005)
Background Worldwide immunization coverage shows an increase in the past years but the validity of the official reports for measuring change over time has been questioned. Facing this problem, donor supported ...
PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology 
Sæbø, Per Eystein; Andersen, SM; Myrseth, Jon; Lærdahl, Jon Kristen; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2005)
PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith–Waterman ...
Analysing the quality of routine malaria data in Mozambique 
Chilundo, Baltazar; Sundby, Johanne; Aanestad, Margunn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2004)
Background In Mozambique, malaria is the principal cause of morbidity and mortality. Efforts are being made to increase control activities within communities. These activities require management decisions ...
Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance 
Nygaard, Vigdis; Løland, Anders; Holden, Marit; Langaas, Mette; Rue, Håvard; Liu, Fang; Myklebost, Ola; Fodstad, Øystein; Hovig, Eivind; Smith-Sørensen, Birgitte (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2003)
Background A limiting factor of cDNA microarray technology is the need for a substantial amount of RNA per labeling reaction. Thus, 20–200 micro-grams total RNA or 0.5–2 micro-grams poly (A) RNA is typically ...
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data 
Wang, Junbai; Bø, Trond H; Jonassen, Inge; Myklebost, Ola; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2003)
Background Using DNA microarrays, we have developed two novel models for tumor classification and target gene prediction. First, gene expression profiles are summarized by optimally selected Self-Organizing ...
 
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